GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Pseudomonas fluorescens GW456-L13

Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate PfGW456L13_2176 Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51)

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2176
          Length = 364

 Score =  632 bits (1630), Expect = 0.0
 Identities = 317/365 (86%), Positives = 341/365 (93%), Gaps = 1/365 (0%)

Query: 1   MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60
           MSE  +LKALR+RID+LDE++L+LISERARCAQEVARVK AS  + E  VFYRPEREA V
Sbjct: 1   MSE-QELKALRLRIDALDEKVLELISERARCAQEVARVKMASLAEGEVPVFYRPEREAQV 59

Query: 61  LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120
           LK +ME N+GPL NEEMARLFREIMSSCLALEQPL+VAYLGPEGTF+QAAA+KHFGH+VI
Sbjct: 60  LKRVMERNQGPLGNEEMARLFREIMSSCLALEQPLKVAYLGPEGTFTQAAAMKHFGHAVI 119

Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180
           SKPMAAIDEVFREV AGAVNFGVVPVENSTEGAVNHTLDSFLEHD+VICGEVELRIHHHL
Sbjct: 120 SKPMAAIDEVFREVAAGAVNFGVVPVENSTEGAVNHTLDSFLEHDMVICGEVELRIHHHL 179

Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240
           LVGE TKTD I+RIYSHAQSLAQCRKWLDAHYPNVERVAVSSNA+AAKRVK EWNSAAIA
Sbjct: 180 LVGENTKTDSISRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNAEAAKRVKGEWNSAAIA 239

Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300
           GDMAA LYGL++LAEKIEDRP NSTRFL+IG+QEVPPTGDDKTSIIVSM NKPGALHELL
Sbjct: 240 GDMAAGLYGLTRLAEKIEDRPDNSTRFLMIGNQEVPPTGDDKTSIIVSMSNKPGALHELL 299

Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360
           +PFH NGIDLTRIETRPSRSGKWTYVFFID +GHH+DPL+K VLEKI  EAVALKVLGSY
Sbjct: 300 VPFHDNGIDLTRIETRPSRSGKWTYVFFIDFVGHHRDPLVKGVLEKISQEAVALKVLGSY 359

Query: 361 PKAVL 365
           PKAVL
Sbjct: 360 PKAVL 364


Lambda     K      H
   0.319    0.133    0.390 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 504
Number of extensions: 9
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 365
Length of database: 364
Length adjustment: 29
Effective length of query: 336
Effective length of database: 335
Effective search space:   112560
Effective search space used:   112560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate PfGW456L13_2176 (Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51))
to HMM TIGR01807 (pheA: chorismate mutase (EC 5.4.99.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.20854.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20854.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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